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brew / rank 12854

Install mosdepth with Homebrew, Nix, apt

Fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing. Version 0.3.14 via Homebrew; verified 2026-07-13. Also installable with nix: nix profile install nixpkgs#mosdepth.

Install commandSecurity notes

install

Additional install commands

macOS

Homebrewverified · 100%
brew install mosdepth

local Homebrew formula metadata

Linux

Nixverified · 92%
nix profile install nixpkgs#mosdepth

nixpkgs package indexes · pkgs/by-name/mo/mosdepth/package.nix · source: api.github.com

Ubuntu aptverified · 92%
sudo apt install mosdepth

Ubuntu 24.04 LTS package indexes · mosdepth · source: archive.ubuntu.com

overview

Package summary

Fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing

Commands and aliases

  • mosdepth

history

Project history and usage

mosdepth is a command-line tool for fast BAM/CRAM depth and coverage calculation across whole-genome, exome, or targeted sequencing datasets.

Project history

mosdepth was introduced by Brent S. Pedersen and Aaron R. Quinlan in a Bioinformatics paper published online in October 2017 and appearing in the March 2018 issue. The paper presented it as a quick coverage calculator for genome and exome sequencing data.

The implementation is written in Nim and uses HTSlib via hts-nim. Its algorithm tracks alignment chunk starts and ends in chromosome-sized arrays rather than using a pileup engine for every read base.

Adoption history

mosdepth gained adoption because sequencing coverage summaries are a routine need for variant calling QC, copy-number workflows, targeted panels, exomes, and whole genomes. The paper compared mosdepth with samtools, bedtools, and sambamba and showed faster runtime on a 30x genome benchmark.

The official README documents binary releases, Bioconda, Homebrew, and Docker usage, making it straightforward to package in bioinformatics environments and reproducible workflow containers.

How it is used

The CLI consumes position-sorted BAM or CRAM input and can report per-base depth, region summaries from BED files, fixed windows, quantized coverage, coverage thresholds, and distributions.

Users choose mosdepth when they need fast genome-wide or region-based coverage calculation and can accept the memory profile of chromosome-sized arrays.

Why package nerds care

mosdepth is notable to package maintainers because it is a compact compiled bioinformatics binary whose value comes from speed, HTSlib integration, and predictable command-line output files rather than from daemon-style services or configuration.

It is also a representative Nim-based scientific CLI in package-manager ecosystems that otherwise contain many C/C++, Python, and Perl genomics tools.

Timeline

  • 2017: Bioinformatics article published online introducing mosdepth.
  • 2018: Article appears in Bioinformatics volume 34 issue 5.
  • 2025: GitHub wiki FAQ updated.
  • 2026: GitHub releases list a latest release dated April 24, 2026.

Related projects

  • samtools depth, BEDTools genomecov, and sambamba are related depth/coverage tools compared in the official paper and README.
  • HTSlib and hts-nim are implementation dependencies named in the README and paper.

security posture

No protected-tool coverage found yet

No matching local secret-handling manifest was found for mosdepth. Package metadata is still published here so future coverage has a stable package URL.

Install behavior

  • No Homebrew post-install hook is recorded in formula metadata.
  • Homebrew bottle metadata is available for 6 platform targets.
  • Installs with 1 runtime dependencies.
  • Build metadata lists 1 build dependencies.

Recommended review

Before unattended agent use, check whether the tool reads plaintext credentials, writes remote state, publishes artifacts, or shells out to plugins.

executables

Installed executables

CommandKindExposureNote
mosdepthcliglobal executable

freshness

Version and freshness

These signals separate page generation age, package-manager activity, and upstream release comparison. Version lag is warned only when an evidence URL and comparable versions are present.

page generated2026-08-04
manager version0.3.14
manager updated2026-07-13
local dataok
upstreamcurrent
latest detectedv0.3.14

https://github.com/brentp/mosdepth

  • okNo freshness warnings were generated.

install metadata

Package metadata

Package keybrew:mosdepth
Version0.3.14
Package managerHomebrew
Package manager pagehttps://formulae.brew.sh/formula/mosdepth
Homepagehttps://github.com/brentp/mosdepth
Repositoryhttps://github.com/brentp/mosdepth
LicenseMIT
Source archivehttps://github.com/brentp/mosdepth/archive/refs/tags/v0.3.14.tar.gz
Last updated2026-07-13T04:04:09Z
Pulseupdated
Dependencieshtslib
Build dependenciesnim
Bottleavailable (on arm64_linux, arm64_sequoia, arm64_sonoma, arm64_tahoe, sonoma, x86_64_linux)
Homebrew post-installnot defined
Servicenone declared

registry facts

Source database details

Source DatabaseHomebrew formula API
Taphomebrew/core
Full Namemosdepth
Version Scheme0
Revision0
Head VersionHEAD
Bottle Stable Root URLhttps://ghcr.io/v2/homebrew/core
Deprecatedno
Disabledno
Keg Onlyno
URL Keys
  • head
  • stable

source database matches

Other package-manager records

Matches are pulled from external package-manager indexes and kept separate from local Automic Vault package links.

Nix95%

mosdepth

nix profile install nixpkgs#mosdepth
  • normalized package name match
  • Matched by: Mosdepth
nixpkgs package indexes · api.github.com · nixpkgs package indexes: pkgs/by-name/mo/mosdepth/package.nix from https://api.github.com/repos/NixOS/nixpkgs/git/trees/master?recursive=1
Ubuntu apt95%

mosdepth 0.3.6+ds-1

BAM/CRAM depth calculation biological sequencing

https://github.com/brentp/mosdepth

sudo apt install mosdepth
  • Section: universe/science
  • Architecture: amd64
  • 2 dependencies
  • normalized package name match
  • Matched by: Mosdepth
Ubuntu 24.04 LTS package indexes · archive.ubuntu.com · Ubuntu 24.04 LTS package indexes: mosdepth from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz
Ubuntu apt95%

mosdepth-examples 0.3.6+ds-1

Test data for mosdepth

https://github.com/brentp/mosdepth

sudo apt install mosdepth-examples
  • Section: universe/science
  • Architecture: all
  • Source Package: mosdepth
  • normalized package name match
  • Matched by: Mosdepth
Ubuntu 24.04 LTS package indexes · archive.ubuntu.com · Ubuntu 24.04 LTS package indexes: mosdepth-examples from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz

package graph

Links come from deterministic package relationships, av.db category and tag curation, ecosystem matches, and package hub membership.

Related tools

  • htslibRuntime dependency declared by Homebrew.
  • nimBuild dependency declared by Homebrew.

Same workflow

  • bismarkShares pkgdb curated category or tags: bioinformatics, cli, genomics, science, wgs.
  • samtoolsShares pkgdb curated category or tags: bam, bioinformatics, cli, cram, genomics.
  • sambambaShares pkgdb curated category or tags: bam, bioinformatics, cli, genomics, science.
  • augustusShares pkgdb curated category or tags: bioinformatics, cli, genomics, science.
  • perbaseShares pkgdb curated category or tags: bam, bioinformatics, cli, cram, genomics.
  • tabixppShares pkgdb curated category or tags: bioinformatics, cli, genomics, science.

source trail

Generated from repository data

This page is generated by av-web from the private package SQLite artifact built by scripts/generate-pkg-sqlite.py.

Used sources

  • cross-ecosystem install command graph
  • curated package history
  • external package-manager database matches
  • package relationship graph
  • package version freshness
  • package-page enrichment
  • pkg.so package database
  • pkgdb category and tag curation